Common disorders of the human gastrointestinal (Gl) tract, including congenital malformations, inflammatory bowel, celiac and peptic ulcer disease, intestine-specific infections and cancer, result in considerable morbidity and mortality in the United States. Although the pathophysiology of many of these disorders is likely related in fundamental ways to mechanisms of normal gut development, the molecular regulation of cell differentiation and fetal development of the mammalian intestine is poorly understood. This is particularly true for the molecular basis of the interaction between gut epithelium and its underlying mesenchyme, a key regulator of intestinal development and homeostasis. This proposal seeks to exploit recent technological advances to initiate a systematic molecular analysis of mammalian intestinal development and organogenesis; the goals and experimental methods are closely aligned with the outline of RFA #DK-01-023. We will begin by examining quantitative and qualitative changes in the gene transcription profile during the critical interval between 13 and 15 days in mouse gestation, when the gut endoderm undergoes an important cellular transition from a poorly differentiated, pseudostratified tissue into a primitive villous epithelium. Preliminary analysis of two separate Serial Analysis of Gene Expression (SAGE) libraries prepared from these developmental stages reveals statistically significant changes in the expression levels of a surprisingly small number of genes, including several putative regulators of intercellular communication, gene transcription, and intracellular signaling. Some of these changes are presumed to drive the acquisition of cellular fate and morphology and tissue form and function in the developing small bowel. The Specific Aims of the project involve more detailed characterization of these SAGE libraries, a unique resource in the field, with a special view toward identifying some of the critical regulators of early intestinal epithelial differentiation and mesenchymal-epithelial interactions. We further propose to examine the sites of mRNA expression for genes predicted to function in intercellular interactions and hence begin to map key candidate signaling pathways in gut development as a prelude to developing practical strategies to examine gene function more directly. Finally, we will expand this analysis in space and in time, by investigating the dynamic alterations in gene expression at two additional stages in small bowel development, and at parallel stages in development of the stomach and colon. The resulting comprehensive analysis of mammalian gut development, quite possibly the first of its kind, will elucidate some essential aspects of normal developmental processes and should contribute to improved understanding and treatment of common disorders of the Gl tract.